diff options
Diffstat (limited to 'plip/test/test_basic_functions.py')
| -rw-r--r-- | plip/test/test_basic_functions.py | 39 |
1 files changed, 23 insertions, 16 deletions
diff --git a/plip/test/test_basic_functions.py b/plip/test/test_basic_functions.py index 7134f55..ac6a012 100644 --- a/plip/test/test_basic_functions.py +++ b/plip/test/test_basic_functions.py @@ -21,13 +21,17 @@ class TestLigandSupport(unittest.TestCase): def test_dna_rna(self): """Test if DNA and RNA is correctly processed as ligands""" tmpmol = PDBComplex() - tmpmol.load_pdb('./pdb/1tf6.pdb') + tmpmol.load_pdb("./pdb/1tf6.pdb") # DNA ligand four times consisting of 31 parts (composite) - self.assertEqual([len(ligand.members) for ligand in tmpmol.ligands].count(31), 4) - for ligset in [set((x[0] for x in ligand.members)) for ligand in tmpmol.ligands]: + self.assertEqual( + [len(ligand.members) for ligand in tmpmol.ligands].count(31), 4 + ) + for ligset in [ + set((x[0] for x in ligand.members)) for ligand in tmpmol.ligands + ]: if len(ligset) == 4: # DNA only contains four bases - self.assertEqual(ligset, {'DG', 'DC', 'DA', 'DT'}) + self.assertEqual(ligset, {"DG", "DC", "DA", "DT"}) class TestMapping(unittest.TestCase): @@ -36,34 +40,34 @@ class TestMapping(unittest.TestCase): def test_ids(self): """Test if the atom IDs are correctly mapped from internal to original PDB.""" tmpmol = PDBComplex() - tmpmol.load_pdb('./pdb/1vsn.pdb') - bsid = 'NFT:A:283' + tmpmol.load_pdb("./pdb/1vsn.pdb") + bsid = "NFT:A:283" for ligand in tmpmol.ligands: - if ':'.join([ligand.hetid, ligand.chain, str(ligand.position)]) == bsid: + if ":".join([ligand.hetid, ligand.chain, str(ligand.position)]) == bsid: tmpmol.characterize_complex(ligand) s = tmpmol.interaction_sets[bsid] for contact in s.hydrophobic_contacts: - if contact.restype == 'ALA' and contact.resnr == 133: + if contact.restype == "ALA" and contact.resnr == 133: self.assertEqual(contact.ligatom_orig_idx, 1636) self.assertEqual(contact.bsatom_orig_idx, 994) - if contact.restype == 'ASP' and contact.resnr == 61: + if contact.restype == "ASP" and contact.resnr == 61: self.assertEqual(contact.ligatom_orig_idx, 1639) self.assertEqual(contact.bsatom_orig_idx, 448) for contact in s.hbonds_ldon + s.hbonds_pdon: - if contact.restype == 'GLN' and contact.resnr == 19: + if contact.restype == "GLN" and contact.resnr == 19: self.assertEqual(contact.a_orig_idx, 1649) self.assertEqual(contact.d_orig_idx, 153) - if contact.restype == 'CYS' and contact.resnr == 25: + if contact.restype == "CYS" and contact.resnr == 25: self.assertEqual(contact.a_orig_idx, 1649) self.assertEqual(contact.d_orig_idx, 183) - if contact.restype == 'ASN' and contact.resnr == 158: + if contact.restype == "ASN" and contact.resnr == 158: self.assertEqual(contact.d_orig_idx, 1629) self.assertEqual(contact.a_orig_idx, 1199) for contact in s.halogen_bonds: - if contact.restype == 'TYR' and contact.resnr == 67: + if contact.restype == "TYR" and contact.resnr == 67: self.assertEqual(contact.don.x_orig_idx, 1627) self.assertEqual(contact.acc.o_orig_idx, 485) - if contact.restype == 'LEU' and contact.resnr == 157: + if contact.restype == "LEU" and contact.resnr == 157: self.assertEqual(contact.don.x_orig_idx, 1628) self.assertEqual(contact.acc.o_orig_idx, 1191) @@ -72,7 +76,7 @@ class GeometryTest(unittest.TestCase): """Tests for geometrical calculations in PLIP""" def vector_magnitude(self, v): - return numpy.sqrt(sum(x**2 for x in v)) + return numpy.sqrt(sum(x ** 2 for x in v)) # noinspection PyUnusedLocal def setUp(self): @@ -132,4 +136,7 @@ class GeometryTest(unittest.TestCase): def test_cluster_doubles(self): """Tests for mathematics.cluster_doubles""" # Are the results correct? - self.assertEqual(set(cluster_doubles([(1, 3), (4, 1), (5, 6), (7, 5)])), {(1, 3, 4), (5, 6, 7)}) + self.assertEqual( + set(cluster_doubles([(1, 3), (4, 1), (5, 6), (7, 5)])), + {(1, 3, 4), (5, 6, 7)}, + ) |